Organizer is a group of cells that induces and patterns surrounding tissues during embryo development. Previous studies of organizers were mainly based on transplantation of various pieces of tissues. This project first aimed to find out putative organizers using a novel method, which was to characterize organizers based on patterns of syn-expression genes. The differential microarray assays selected a list of gene that are enriched or depleted in three known organizers (Hensen’s node, notochord and floor plate and zone of polarizing activity). Whole-mount in-situ hybridisation, histological sections and optical projection tomography were used to further analyse the expression patterns of these syn-expressed genes. The roof of dorsal thalamus including the pineal gland is revealed as one of a potential organizer, with expression of cNOT1, TSPAN6 and PKIγ. Further studies of gene expression showed that cNOT1 is expressed broadly in early diencephalon and is restricted to pineal gland and its posterior territory till HH25. This raises questions that whether cNOT1 is marking the pineal progenitors and whether there are movements of cNOT1-expressing cells. Fate mapping analysis demonstrates that not all cNOT1-expressing cells are pineal progenitors and they are not moving over the development of pineal gland. Considering the change of gene expression over diencephalon development, it could be that either cNOT1-expressing cells or the pineal gland is a potential organizer. To assess their organizing abilities, ablation experiments were performed on both area. Ablation of pineal progenitors alone led to regeneration of the whole pineal gland and with normal expression patterns of diencephalic genes. On the other hand, removal of all cNOT1-expressing cells inhibited the regeneration of pineal gland. In conclusion, these data suggest that the pineal gland can be regenerated from surrounding tissues. Whether the roof of the dorsal thalamus or the cNOT1-expressing cells is an organizer requires more experiments, including transplantation, to assess.